TABLE 1.

List of MD simulations performed for each condition

Simulations of the wild-type LeuT are denoted as WT, and the ones with mutations are denoted as Y268A, R5A, and D369A. The presence of either Na⁺ or Li⁺ in the simulation conditions is denoted as Na or Li, respectively; and the presence or absence of substrate is denoted as Leu/Ala or ns, respectively. All molecular dynamics simulations were started from the crystal structure of LeuT in the occluded state (PDB code 2A65).

Condition	Number of replicas	Total simulation time
		ns
WT.Na.Leu	2	590
WT.Na.Ala	1	360
WT.Na.ns	3	3600
WT.Li.Leu	1	480
WT.Li.Ala	1	480
WT.Li.ns	2	2400
Y268A.Na.Leu	1	600
Y268A.Na.ns	3	4320
R5A.Na.ns	2	2640
D369A.Na.ns	3	2480
Total	19	17,950